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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><a href="http://matdl.org/matdlwiki/index.php/softmatter:Radial_Distribution_Function">http://matdl.org/matdlwiki/index.php/softmatter:Radial_Distribution_Function</a><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>That tells you what a rdf is and what the units are.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>It is a probability function, so your graph is saying that you are 25 times more likely to find the tails 1 nm from the center versus in the bulk.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>If you want a density, then you are going to have to do some subsequent processing to the data that the g_rdf script provides you.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Catch ya,<br><br>Dr. Dallas Warren<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Medicinal Chemistry and Drug Action<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>, Monash University<br>381 Royal Parade, Parkville VIC 3010<br>dallas.warren@monash.edu<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>+61 3 9903 9304<br>---------------------------------<br>When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>sa<br><b>Sent:</b> Tuesday, 1 March 2011 6:11 AM<br><b>To:</b> gmx-users@gromacs.org<br><b>Subject:</b> [gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf.<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Dear GMXusers, <br><br>Last week, i asked a question about the calculation of average radial density functions relative to the center of mass of a micelle formed with DPC molecules (rdf). Unfortunately i received no response. So i re ask my question. So I would like to obtain the average rdf function (in g/cm3) for different groups of my micellar system (such as the headgroup, alkyl tail of the surfactant and water). For this purpose, I have created a index file where all DPC atoms (heavy and H atoms ) are separated in different groups and use the following command with g_rdf (4.5.3)<br><br>g_rdf_mpi -f *_Center_All.xtc -s run_1.tpr -o DPC-Self-AMB_100-155ns_DPC_RDF.xvg -b 100000 -e 155000 -norm -com -n index_Radial_Profile_DPC.ndx <br><br>I chose DPC atoms as a reference group and obtain the rdf curves for the DPC headgroup, alkyl tail and water. I obtain the following figure : <br><br><a href="http://img4.hostingpics.net/pics/213680DPCSelfAMB100155nsRDF.jpg">http://img4.hostingpics.net/pics/213680DPCSelfAMB100155nsRDF.jpg</a><br><br>I don't understand why the curves amplitudes for the headgroup, alkyl tail are so high (and what is the unity ?), For example for the C12 alkyl chain rdf I understand well the help of the g_rdf tool, I expect a rdf with a density maxima around 0.8 - 0.9 g/cm3. Did i compute the expected function with above command ? If not, how to obtain the rdf (in g/cm3) for each components ?<br><br>Thanks for the help. <br><br>SA <o:p></o:p></p></div></div></body></html>